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C++ tool inside Singularity container: direct execution fine but execution within Bash script inside same container crashes with illegal instruction

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0

I'm facing a weird issue when running a C++ executable (Gromacs tool editconf) that was cross-compiled inside a Singularity container. The container was built on my local machine and transferred to a small computing cluster where I observe the following:

When I directly execute the Gromacs command ("gmx editconf" with a couple of arguments), it works fine:

singularity exec image.simg gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

But as soon as I try to execute it via a Bash script inside the container

singularity exec image.simg /bin/bash /opt/prep_stuff.sh $ARG1 $ARG2

which in turn executes the Gromacs tool like this

gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

it crashes with the error

/opt/prep_stuff.sh: line 109: 27326 Illegal instruction (core dumped) gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

while all the other steps in that Bash script are correctly carried out. Also, line 109 (begin of a for loop) appears far before the actual call of gmx editconf.

Does anyone have an idea about why the two approaches behave that differently although executed on the same machine? I need it to work following the Bash script approach.

Many thanks!

c++ bash cluster-computing singularity-container

share|improve this question

edited Mar 25 at 7:28

user3305567

asked Mar 25 at 0:19

user3305567user3305567

83

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  ok, i just changed the compiler flag to a low SIMD level (SSE2) and now it works. however, i'm still wondering, why one of the two approaches (without intermediate bash script) ran on the same cluster without having set the compiler flag to some low optimization level.
  
  – user3305567
  Mar 25 at 14:15
  

  
  
  
  

add a comment | 

0

I'm facing a weird issue when running a C++ executable (Gromacs tool editconf) that was cross-compiled inside a Singularity container. The container was built on my local machine and transferred to a small computing cluster where I observe the following:

When I directly execute the Gromacs command ("gmx editconf" with a couple of arguments), it works fine:

singularity exec image.simg gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

But as soon as I try to execute it via a Bash script inside the container

singularity exec image.simg /bin/bash /opt/prep_stuff.sh $ARG1 $ARG2

which in turn executes the Gromacs tool like this

gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

it crashes with the error

/opt/prep_stuff.sh: line 109: 27326 Illegal instruction (core dumped) gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

while all the other steps in that Bash script are correctly carried out. Also, line 109 (begin of a for loop) appears far before the actual call of gmx editconf.

Does anyone have an idea about why the two approaches behave that differently although executed on the same machine? I need it to work following the Bash script approach.

Many thanks!

c++ bash cluster-computing singularity-container

share|improve this question

edited Mar 25 at 7:28

user3305567

asked Mar 25 at 0:19

user3305567user3305567

83

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  ok, i just changed the compiler flag to a low SIMD level (SSE2) and now it works. however, i'm still wondering, why one of the two approaches (without intermediate bash script) ran on the same cluster without having set the compiler flag to some low optimization level.
  
  – user3305567
  Mar 25 at 14:15
  

  
  
  
  

add a comment | 

I'm facing a weird issue when running a C++ executable (Gromacs tool editconf) that was cross-compiled inside a Singularity container. The container was built on my local machine and transferred to a small computing cluster where I observe the following:

When I directly execute the Gromacs command ("gmx editconf" with a couple of arguments), it works fine:

singularity exec image.simg gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

But as soon as I try to execute it via a Bash script inside the container

singularity exec image.simg /bin/bash /opt/prep_stuff.sh $ARG1 $ARG2

which in turn executes the Gromacs tool like this

gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

it crashes with the error

/opt/prep_stuff.sh: line 109: 27326 Illegal instruction (core dumped) gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

while all the other steps in that Bash script are correctly carried out. Also, line 109 (begin of a for loop) appears far before the actual call of gmx editconf.

Does anyone have an idea about why the two approaches behave that differently although executed on the same machine? I need it to work following the Bash script approach.

Many thanks!

c++ bash cluster-computing singularity-container

share|improve this question

edited Mar 25 at 7:28

user3305567

asked Mar 25 at 0:19

user3305567user3305567

83

singularity exec image.simg gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

singularity exec image.simg /bin/bash /opt/prep_stuff.sh $ARG1 $ARG2

gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

/opt/prep_stuff.sh: line 109: 27326 Illegal instruction (core dumped) gmx editconf -bt octahedron -f complex.pdb -o complex.pdb -box 8

share|improve this question

edited Mar 25 at 7:28

user3305567

asked Mar 25 at 0:19

user3305567user3305567

83

share|improve this question

edited Mar 25 at 7:28

user3305567

asked Mar 25 at 0:19

user3305567user3305567

83

asked Mar 25 at 0:19

user3305567user3305567

83

asked Mar 25 at 0:19

user3305567user3305567

83